Directed evolution gets a significant speed boost

Synthetic biology attempts to generate biomolecules with new and/or improved activities for use as, say, drugs or fuel. One way of producing new biomolecules involves directed evolution, in which specific functions are selected for, but that has been slow and labor intensive. A faster method comes from Esvelt et al. at Harvard, who have devised a system for directed evolution that is rapid and continuous, cycling through twenty to thirty rounds of selection in a single day without human intervention.

The new system relies on phage, viruses that infect bacteria, and is thus called "phage-assisted continuous evolution"—yielding the apt acronym PACE. In this system, molecules from E. coli flow through an evocatively named "lagoon" filled with phage. Each phage contains a copy of the Gene Of Interest (GOI), the one that will undergo directed evolution.

Being viruses, the phage can’t replicate DNA on their own; they need to get into a bacterial cell to do that. In order to successfully infect a bacterium—to not only get into the E. coli cell, but to force it to make more phage and spew them out—the phage require a protein called pIII.

To force the GOI to evolve, the researchers took the gene for pIII out of the phage and put it into the bacteria, linking its expression to the activity of the GOI. Thus, phage containing more active versions of the GOI will generate more pIII, and will be more infectious, spreading more copies of that version of the GOI as they infect more hosts. Eventually, only the most successful mutant version(s) of the GOI will be left. To speed things up a bit, the bacteria are also given a "mutagenesis plasmid" that suppresses DNA proofreading, which increases the mutation rate.

The research team demonstrated PACE’s speed by evolving a number of variants of T7 RNA polymerase, a well studied enzyme responsible for transcribing DNA into RNA. T7 RNA polymerase binds to a very specific DNA sequence, the T7 promoter, and transcribes only those genes preceded by this sequence. Esvelt et al. rendered pIII production dependent on the protein binding to a different sequence.

After a week of PACE that encompassed 200 rounds of evolution, the team made T7 RNA polymerase that bound to the alternate promoter, sometimes with higher activity than it has on its native target.

Two different PACE experiments were carried out concurrently in separate lagoons, and although both eventually made the same mutant T7 RNA polymerase, they took different routes to get there. The scientists also made T7 RNA polymerase mutants that initiated transcription with ATP or CTP instead of the GTP it prefers; these took only 36 hours.

The authors note that “the PACE system can be assembled entirely from a modest collection of commercially available equipment and does not require the manufacture of any specialized components,” making it ideal for those DIY bio types hanging out in Brooklyn. In literally bringing directed evolution up to speed, PACE may also help answer questions about molecular evolution as it occurs in nature while generating new biomolecules with desirable activities and traits.

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

Isn't this really just selective breeding, meaning, it's just doing what it was already meant to do which is become selective to certain things in its environment. Think of it as a socket set with a detachable head, it's designed to do that, just becuase you're changing the head by selective pressure doesn't not mean it's actually gaining any new abilities that it wasn't already able to do beforehand, hence no evolution.

Even ignoring that, trying to use such a simple thing as a virus to prove incredibly, beyond human understanding, engineering problems of incredibly complex organisms and co-dependent chemistry systems and organs etc, and the countless other independently 'evolving' species seems to be a gross oversimplification, to even be as if grasping at straws.

Hmmm... I wonder if it would be asking too much for them to evolve a bug that can turn sunlight/any form of radiation, water and CO2 into butanol or hexanol very efficiently and close to carbon neutrally? I am hoping for an overall energy efficiency better than any photovoltaics. Or at least much better than natural photosynthesis. (EDIT: kidding...sort of... I do want this badly)

In any case... this is an excellent advance for synthetic biology. Due to biology's complexity, engineering biological systems was always going to be a mixture of design and evolutionary methods.

Hmmmm.. next step make a a bacterium evolve a totally new characteristic. Adda protein or even a whole metabolic pathway to its repertoire.

After reading the title, I could not help but wonder what if we introduced some mutation that lead these bugs to become sentient, and then they started to wonder how they came to be, and then some twit of a fundamentalist bug postulated it was too big a jump, there had to be an intelligent creator's god like hand designing things ... and he would be right.

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

My English is pretty good for a Dutchman (hell, I even use capitals! ) but I have no idea what word you are talking about.

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

Is your <shift> key broken? As an English teacher and one-time editor of an ESL grammar book, I can tell you that the language skills of all Ars authors, on their worst day, is better than yours.

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

Is your <shift> key broken? As an English teacher and one-time editor of an ESL grammar book, I can tell you that the language skills of all Ars authors, on their worst day, is better than yours.

I don't see the relevance. Perhaps his English sucks, and yes perhaps so does his grammar; but in what way does that have any relevance on what he's saying?

He's not trained to pick up on these errors, yet they're so glaring he's noticed them. Do I care? No, not really. So long as I can easily understand the story and the facts are accurate enough, I couldn't care less.

Now, I know a few ex-English teachers; and I've worked with several people in the editing field before. They're painful to talk or write to, because they have an incessant need to correct everyone around them when improper English is used. I notice you don't comment on the issues with the post. What does this tell us about your qualifications in this area?

Hmmm... I wonder if it would be asking too much for them to evolve a bug that can turn sunlight/any form of radiation, water and CO2 into butanol or hexanol very efficiently and close to carbon neutrally? I am hoping for an overall energy efficiency better than any photovoltaics

I'm not sure that's possible. Particularly when you need to burn said butanol or hexanol to get the energy back as something useful (ie: electricity). This process looses quite a bit of energy.

Better to suggest using this technique to find a more efficient form of photovoltaic. Either way, it's going to involve much more than a single "gene of interest".

Quote:

you guys are posting too much, about too many games, and your signal/noise is way out of wack.

Let me get this straight. The greater appearance of typos in articles is due to posting too much about... games? Even though the games-related articles are written by completely different people from the other articles?

And the frequency of posting is a problem, even though Nobel Intent only posts maybe 1-2 articles a day?

Sorry, I'm not buying it.

Also, "signal" and "noise" are in the eyes of the beholder. For you, posting about games may be "noise", but it's "signal" for many others.

Quote:

Perhaps his English sucks, and yes perhaps so does his grammar; but in what way does that have any relevance on what he's saying?

You are correct that it isn't relevant. However, when you call someone out for their poor grammar, it is generally a very good idea to not exhibit equally bad or worse grammar than the person you're calling out. It draws attention to your own mistakes and deflects from the point at hand.

Quote:

Now, I know a few ex-English teachers; and I've worked with several people in the editing field before. They're painful to talk or write to, because they have an incessant need to correct everyone around them when improper English is used. I notice you don't comment on the issues with the post. What does this tell us about your qualifications in this area?

Or, you know, maybe he's just not the kind of ex-English teacher who constantly corrects people's writing. Maybe he realized that going around correcting people would cause others to avoid him, so he doesn't do it.

Or maybe he found the post in question's English skills to be far, far worse than the Ars article, and therefore in greater need of correction.

Hmmm... I wonder if it would be asking too much for them to evolve a bug that can turn sunlight/any form of radiation, water and CO2 into butanol or hexanol very efficiently and close to carbon neutrally? I am hoping for an overall energy efficiency better than any photovoltaics. Or at least much better than natural photosynthesis. (EDIT: kidding...sort of... I do want this badly).

Just for the record, you just noted that an idealized, test-tube evolution experiment resembles the design of computer algorithms inspired by idealizations of evolutionary theory. . . to me that sounds like saying strawberries taste alot like strawberry flavored candy :-)

Hmmm... I wonder if it would be asking too much for them to evolve a bug that can turn sunlight/any form of radiation, water and CO2 into butanol or hexanol very efficiently and close to carbon neutrally? I am hoping for an overall energy efficiency better than any photovoltaics. Or at least much better than natural photosynthesis. (EDIT: kidding...sort of... I do want this badly)

Cyanobacteria already do, except they kick out sugars instead of alcohols. They still burn and can be modified into alcohols if you so desire.

You may have misunderstood me... what I mean by carbon neutral is that the whole energy "eco-system" surrounding this will in total be carbon neutral.

Yes you produce CO2 when you burn the fuels... and that same CO2 gets used up when producing the fuels... basically this is just a form of solar energy. The fuel is a mere conduit, the bacterium a collector.

@Alan Chen

Duly noted! lol. I got it in reverse of course... GA is little more than digital selective breeding, which is a form of directed evo. But what I was getting at was... this form of directed evolution is much faster, so we could use it in our engineering efforts in similar ways to GA. Selective breeding that does not takes years, or generations, would be a boon to synthetic biology.

Hmmm... I wonder if it would be asking too much for them to evolve a bug that can turn sunlight/any form of radiation, water and CO2 into butanol or hexanol very efficiently and close to carbon neutrally? I am hoping for an overall energy efficiency better than any photovoltaics. Or at least much better than natural photosynthesis. (EDIT: kidding...sort of... I do want this badly)

Cyanobacteria already do, except they kick out sugars instead of alcohols. They still burn and can be modified into alcohols if you so desire.

Yes am aware of that... but what I was getting at is an organism that can convert to a liquid chemical fuel as well, and do the photosynthesis more efficiently than is natural.

Isn't this really just selective breeding, meaning, it's just doing what it was already meant to do which is become selective to certain things in its environment. Think of it as a socket set with a detachable head, it's designed to do that, just becuase you're changing the head by selective pressure doesn't not mean it's actually gaining any new abilities that it wasn't already able to do beforehand, hence no evolution.

It is clear from this post that you don't understand what evolution is. Let me help:

Evolution is defined as a change in allele (gene) frequencies in a population over time.

That is all. No requirements for new features. Nothing said about making new species. This is what evolution IS.

It is the effect of evolution that such changes can cause new features to arise or cause previously compatible populations to become reproductively isolated, thus fulfilling the biological species concept definition of new species. These things can happen, but they are not a requirement for evolution, simply a result of it.

What causes the changes in gene frequencies can be anything from selection (both natural and artificial selection; selective breeding is included in the latter) to random drift to horizontal gene transfer to combinations of all three. But, as long as there is genetic change in a population over time, then that population can be said to be evolving. It doesn't matter if it is all random neutral drift due to silent of neutral changes in the genome, or if it is hardcore positive selection of strongly advantageous or against strongly disadvantageous traits. If it is causing a genetic change in the population over time, it falls under the umbrella of evolution.

So to draw the conclusion, and I quote, "hence no evolution" from the premise "this is just selective breeding" is EXACTLY wrong.

Telekinesis wrote:

Even ignoring that, trying to use such a simple thing as a virus to prove incredibly, beyond human understanding, engineering problems of incredibly complex organisms and co-dependent chemistry systems and organs etc, and the countless other independently 'evolving' species seems to be a gross oversimplification, to even be as if grasping at straws.

What the hell does that have to do with anything at all in this article?

So it's not 'intelligent design' if this were to lead to new species... instead this is 'directed evolution'. I think I see what you did there ;-)

Intelligent Design would involve having the designer (in this case, can I assume you are talking about the researchers doing this work?) actually going in designing/writing the desired gene sequences, rather than setting up a system to promote rapid evolution (via poor proofreading and thus enhanced mutation rates, along with the system self-selecting the most successful resulting genes) and letting it do its thing, wouldn't it?

I admit, I am fuzzy on just what Intelligent Design proponents postulate their designer to be doing...

Directed evolution sounds to me a lot like artificial selection or selective breeding (both of which are, contrary to what some seem to think, mechanisms of evolution), but in this case at the molecular level focusing on single genes. No?

[edit]And, I'd just like to reiterate that it is not a requirement for evolution to give rise to new "species" (which is an arbitrarily defined term, anyway). That's simply one of the many possible effects of evolution.

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

You will note that even publications like the New York Times suffer from more grammatical and typographical errors than they once did. Copy editors cost money, and the copy editing process itself costs money. If the choice is between a copy editor and a few dozen articles, I'll take the articles.

Mesago wrote:

Now, I know a few ex-English teachers; and I've worked with several people in the editing field before. They're painful to talk or write to, because they have an incessant need to correct everyone around them when improper English is used. I notice you don't comment on the issues with the post. What does this tell us about your qualifications in this area?

I'd wager I know at least as many as you do, and the only time I've had my grammar, spelling, or diction corrected is when I've asked for it.

Even ignoring that, trying to use such a simple thing as a virus to prove incredibly, beyond human understanding, engineering problems of incredibly complex organisms and co-dependent chemistry systems and organs etc, and the countless other independently 'evolving' species seems to be a gross oversimplification, to even be as if grasping at straws.

What the hell does that have to do with anything at all in this article?

I think that was one of those "you can't use this study to prove evolution exists" comments.

This appeal to complexity and the severe limits of human understanding is often used when a commenter does not accept the basic premise of the scientific research (in this case evolution). You can find similar comments on articles involving anthropogenic climate change.

The big challenge with directed evolution is not in finding molecules that bind to a particular target-including transition states- but figuring out how to get them to do something biologically useful. Aptamers (molecules that bind to specific targets) have been around since about 1990. Aptamers can distinguish, for example, between caffeine and theophylline which differ by a single methyl group and aptamers can and have been found to a wide range of molecules.Delivery is the problem. The aptamers are big, expensive and hard to get into the cells of interest. This new technology is a bit of an aid in helping find aptamers but doesn't do much for the delivery problems.

I have found that the SNR for Ars is great AND I absolutely love the fact that I can read science and game related news on a single site. I would love to see more EE science related articles, but the recent semiconductor ones were nice.

I have found that the SNR for Ars is great AND I absolutely love the fact that I can read science and game related news on a single site. I would love to see more EE science related articles, but the recent semiconductor ones were nice.

+ I just wish the science section got more love...

I wouldnt mind them posting articles that are similar to the science shows about space and what not on the Science Channel and NatGeo, only not dumbed down. The next time I see a visual depicted a black hole as a whirl pool or a scientist talk about a singularity, I will shit myself and throw it at the TV....

it used to be that i would hardly ever find a typo error in an ars article. usually, any errors at all were found in long, multi-page articles. it's pretty much inexcusable to have a blatant extra word clearly out of context in a single page article here at ars, such as the one above. you know, something that someone would find if they bothered to read the article through once before they posted it.

you guys are posting too much, about too many games, and your signal/noise is way out of wack. i'm not posting because it's just this one error, i'm posting because the errors are mounting up. if you're playing some game trying to make a case against plagiarists, then fine, but your quality is still slipping overall.

Is your <shift> key broken? As an English teacher and one-time editor of an ESL grammar book, I can tell you that the language skills of all Ars authors, on their worst day, is better than yours.

People like Telekenesis (sic) are really just talking to themselves when they spew that intelligent design junk. They know the rest of the world is never going to agree with them, but they want validation. I say, if you don't accept evolution, that's fine, but kindly refrain from bothering the rest of us.

Why are people so worried about this. 200 generations of E.Coli with an artificially higher mutation rate? There are literally billions of new generations of E.Coli created every day in the world. It's much more likely that E.Coli will evolve into something problematic in the wild than in the lab.

I just want to say that, while I would never object to more general science in all flavors articles on ArsTechnica, the science section gets plenty of love. ArsTechnica science articles are some of the most lucid, clear, and easy to read science articles on the internet. I would never object to more, but I am quite happy with the treatment thus far.